Saturday, February 6, 2010

Do You Believe in Magic? How Evolution Creates Evolution

New research is suggesting yet another twist on how evolution creates itself. The research tells us more about epigenetics, so first we need to review how epigenetics has already falsified much of evolutionary theory. I’ve written this before but it bears repeating. The adaptation of species to environmental pressures would seem like obvious evidence for evolution. But in recent years we have begun to understand the enormous complexity of adaptation. It is not a story of natural selection acting on undirected biological variations (that is, variations that are blind to environmental pressures). This sort of undirected process has been the evolutionary dogma for the past century. In what was known as the Modern Synthesis, biological adaptation was described as resulting from blind variations resulting, for instance, from genetic rearrangements or unguided mutations. No thanks to evolution we are now beginning to understand the real version of biological adaptation. What we are seeing is an incredibly complex adaptation machine that tweaks the designs of organisms in response to environmental pressures.

It is not a simple story as there are a variety of different ways such adaptations can occur. These mechanisms, broadly labeled as epigenetic inheritance, can regulate the expression of genes as well as redesign the genes. The bottom line is that the adaptations are not unguided, they benefit the organism, and they are extremely complex. The evolutionary story is completely wrong. As one evolutionist admitted, the Modern Synthesis:

states that variations are blind, are genetic (nucleic acid-based), and that saltational events do not significantly contribute to evolutionary change. The epigenetic perspective challenges all these assumptions, and it seems that a new extended theory, informed by developmental studies and epigenetic inheritance, and incorporating Darwinian, Lamarckian, and saltational frameworks, is going to replace the Modern Synthesis version of evolution.

A new extended theory? This should be interesting, for it would have to explain how evolution creates mechanisms which, themselves, cause evolution (in the form of adaptation). I sense a just-so story coming on. In fact, evolutionists are already explaining this without losing a step. For instance (from the same paper):

Epigenetic inheritance should be favored in fluctuating environmental conditions that last for more than one generation (but not for very long) and may be particularly important in the type of environments experienced by many microorganisms. In such fluctuating environments, efficient epigenetic inheritance is likely to evolve (i) if the parental environment carries reliable information about the offspring’s environment, (ii) when the response to induction is lengthy and incurs a very high cost, and (iii) when recall is not an option or incurs too high a cost.

See, that was easy. Evolution just happens. So long as there is an advantage to a new design, then it will appear. That's how evolution works.

One of the best known epigenetic mechanisms is DNA methylation in which a methyl group is added to cytosine, one of the four DNA chemical letters. The methyl group is a sort of marker that can help to regulate the expression of genes. DNA methylation is accomplished via the action of a complicated molecular machine (DNA methyltransferase) that adds the methyl group at precisely the right location in the DNA strand.

So evolution configured DNA methyltransferase and the associated molecular information that tells it where to add the methyl group, so that later the organism and its offspring could benefit when certain environmental pressures arose. That's good planning--evolution is almost as smart as evolutionists are.

And to further complicate matters, this molecular marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information to the epigenetic mechanism. In this case, the methyl group is hydroxylated. And of course a different complicated molecular machine is required for the task, and the information of when and where to go to work is needed.

Evolution must have created all these processes and molecular machines so evolution could occur. But that’s not all. Recently researchers found differing methylation patterns amongst mice from the same litter, reared in the same environment. As was reported:

[Researchers] found regions in the animal's genetic makeup with strikingly different patterns. Moreover, these regions occurred among genes responsible for determining anatomy during early development.

In other words, variably methylated regions of DNA have been discovered, and such variability could lead to increased trait variability. Evolutionists speculate that this could help the population survive:

We're proposing that certain gene variants contribute to heterogeneity in populations. In a fluctuating environment, this gives generations more opportunity to survive.

And perhaps this new capability could help answer long-standing questions about how it is that evolution could work so well. As the article explains:

For more than 100 years, mainstream science has embraced the basic tenets of Darwin's view that characteristics that increase an organism's ability to survive and reproduce will be passed from generation to generation. … Characteristics that affect an organism's ability to adapt and survive in times of environmental change have been thought to arise by chance through random mutations in an organism's DNA. However, this view could not explain how such mutations, which arise only rarely, help organisms of every size and variety adapt quickly enough through time.

We already knew evolution was plenty clever. It created genes, chromosomes and alleles, horizontal gene transfer, introns, DNA methylation, and its additional hydroxyl signal just to name a few structures and processes. Of course there is a dizzying array of molecular machines choreographing this drama at just the right moments. All this so more evolution could occur.

And now we add another miracle to the list: variably methylated regions of DNA so future generations could survive when some unforeseen environmental challenge arises. The levels of absurdity to which evolutionists will go is truly remarkable.

Cell differentiation is due to epigenetic factors, and even epigenetic inheritance apparently only lasts a few generations. All of this can be considered as part of the phenotype from a theoretical perspective—unless it can be shown to lead to a permanent change in genotype. In which case, as it would be a form of Lamarckian inheritance, it might still be consistent with evolution, though not neodarwinism.

Whether epigenetic inheritance is only temporary or whether it leads to permanent change, the complex mechanisms involved would seem to be a huge challenge to neo-Darwinian theory, and would seem to fit more easily into a design hypothesis.

Bilbo: Whether epigenetic inheritance is only temporary or whether it leads to permanent change, the complex mechanisms involved would seem to be a huge challenge to neo-Darwinian theory, and would seem to fit more easily into a design hypothesis.

Why? It's not as if evolution can't create complex mechanisms. We already have a huge amount of data supporting evolution, and nothing supporting design, so supposing design would require some very specific entailment.

There you go again, another example of how evolution is at war with science.

" unless it can be shown to lead to a permanent change in genotype."

There's evolutions fixation on genes. Of course epigenetics can cause permanent change, but evolutionists are in denial about it.

"It's not as if evolution can't create complex mechanisms."

There is no scientific evidence evolution can create epigenetic mechanisms. And not only did evolution doesn't predict them, it predicts they would not evolve since they convey no fitness improvement for eons. Nothing makes sense in biology in light of evolution.

Cornelius Hunter: There you go again, another example of how evolution is at war with science.

Gee whiz. The use of the term "genotype" was meant broadly, that is, the heredity of an organism. Unless the facility can be shown to be transmitted reliably to future generations, it can be considered as part of the phenotype from a theoretical perspective.

Cornelius Hunter: Of course epigenetics can cause permanent change, but evolutionists are in denial about it.

Possibly. But that may just mean something like Lamarckian evolution, and even then it may only work primarily on certain traits, e.g. evolution in response to rapidly evolving pathogens.

Cornelius Hunter: There is no scientific evidence evolution can create epigenetic mechanisms.

Of course there is.

Cornelius Hunter: And not only did evolution doesn't predict them, it predicts they would not evolve since they convey no fitness improvement for eons.

Is it OK if I just call you Tim? I prefer Mike Gene's approach for testing design hypotheses: How Discontinuous is its origin with natural processes? How analagous to Design processes? How Rational is it? How much Foresight does it exhibit?

Zach, epigenetic processes in prokaryotes? This would make Mike so happy.

Bilbo: epigenetic processes in prokaryotes? This would make Mike so happy.

We have every reason to believe epigenetic gene control is ancient, and that it evolves like everything else. And if it was already functional in primitive organisms, along with intracellular and intercellular signaling, that lends support to the theory that metazoa has deep roots.

Zach: We have every reason to believe epigenetic gene control is ancient, and that it evolves like everything else. And if it was already functional in primitive organisms, along with intracellular and intercellular signaling, that lends support to the theory that metazoa has deep roots.

"The adaptation of species to environmental pressures would seem like obvious evidence for evolution."

It is.

"But in recent years we have begun to understand the enormous complexity of adaptation. It is not a story of natural selection acting on undirected biological variations (that is, variations that are blind to environmental pressures)."

Random variation causes differential survival and reproductive success among the individuals of a population. Those whose variation makes them fitter than others leaving a greater genetic legacy. Consequently, the population becomes more adapted to its environment over time.

"In what was known as the Modern Synthesis, biological adaptation was described as resulting from blind variations resulting, for instance, from genetic rearrangements or unguided mutations."

In what is still known as the modern synthesis, biological adaptation occurs as I described above. The variations are random, but the differential fitness they cause leads to non-random natural selection.

"No thanks to evolution we are now beginning to understand the real version of biological adaptation. What we are seeing is an incredibly complex adaptation machine that tweaks the designs of organisms in response to environmental pressures."

Yes, as I have just explained.

Evolution can create complexity from simple beginnings, given enough time (no, 6000 years is not long enough). No one has said that epigenetics is a prerequisite for evolution--only that once established it can, like any character, evolve to be more adaptive and/or efficient.

Bilbo said: "s it OK if I just call you Tim? I prefer Mike Gene's approach for testing design hypotheses: How Discontinuous is its origin with natural processes? How analagous to Design processes? How Rational is it? How much Foresight does it exhibit?"

You can call me TIm. It's not actually my real name anyway! Sorry, but who is Mike Gene? Do you have a link to his testing design approach?

"We have every reason to believe epigenetic gene control is ancient, and that it evolves like everything else."

Sure, these complicated machines and processes might be needed in the far future--so they evolve. That's just how evolution works. What's really strange is that evolutionists were in denial of epigenetics for so long. Strange, it fits their theory so well.

Cornelius Hunter: Sure, these complicated machines and processes might be needed in the far future--so they evolve. That's just how evolution works.

No, they have a function in the primitive organism, just like they do in extant prokaryotes. Again, you can't look at each datum in isolation. We have strong evidence of Common Descent and mechanisms of descent with modification, including the evolution of complex structures. You can suppose whatever you want, but the evidence supports evolution of epigenetics.

The reason for repeating it is that you continue to take isolated bits of evidence, but ignore the overall patterns—even when there have been attempts to engage those patterns on the appropriate threads. We have to start with what we can establish with some certainty, and that includes Common Descent as it applies to most taxa.

"More On Evolution In The Still RNA World"http://www.the-scientist.com/community/posts/list/260/122.page#4818

Fitting together the pieces of the "still an RNA world" puzzle ?

- Rational probability and possibility that the initial, independent pre-biometabolism direct sunlight-fueled genes (life) were RNAs, who evolved their DNA-images as operational patterns-manuals libraries, and celled and genomed them. They most probably synthesized (and nucleusized) their DNAs manual libraries as their functional organs, to serve as their environmentally stabler than RNA, than themselves, works memory cores.

- Rational possibility that ALL RNAs represent the original archae-genes that since their (life) genesis have been and still are the primary actors, assessors, messengers, operators of all life processes.

- Rational possibility that the RNAs are the environmental feedback communicators to, and modifiers of, the genomes, that the RNAs are the effectors of the desirable biased genes expressions modifications, of enhanced energy constraining for survival.

I recently tweeted and stumbled upon your post. Really your post is very informative and I enjoyed your opinions. Do you use twitter or stumbleupon? So I can follow you there. I am hoping you post again soon.

Di Mauro's RNA formation concept is great. But, a step further, how had the RNA become alive, i.e. how did it (1) uptake the sun's radiation and how did it (2) catalytically use it to perform work, to keep augmenting its constrained energy by keeping augmenting its self-propagation, which is the essence of Life ?

THIS IS THE STILL MISSING TWIST IN THE BRANCHING OF LIFE FROM OTHER SURVIVING, ENERGY DIGESTING, MATTER SUCH AS BLACK HOLE. THIS TWIST IS THE BIOLOGICAL ENTITY "CULTURE", LEARNING-ADAPTING, THE ESSENCE OF DARWINIAN EVOLUTION SINCE LIFE'S DAY ONE. THIS MUST HAVE BEEN THE CRUCIAL PROCESS TWIST, EVEN WITHOUT YET KNOWING ITS MECHANISM.

Or, is the mechanism of this twist known now?It is now known how the RNAs, Earth's primal organisms, adopt an enhanced energy event's DNA conformation. But what is the mechanism of its recognizing the enhanced energy event?